Package: RTopper

Version: 1.28.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTopper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RTopper_1.28.0.tar.gz

StartedAt: 2019-04-13 05:14:35 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:17:15 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 160.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RTopper.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTopper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RTopper_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTopper.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTopper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTopper' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'RTopper' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6L6yAq/R.INSTALL15b8262d4594/RTopper/man/fgsList.Rd:37: file link 'org.Hs.eg' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6L6yAq/R.INSTALL15b8262d4594/RTopper/man/fgsList.Rd:41: file link 'GO' in package 'GO.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6L6yAq/R.INSTALL15b8262d4594/RTopper/man/fgsList.Rd:42: file link 'KEGG' in package 'KEGG.db' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTopper.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'limma'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeScore: no visible global function definition for 'glm'
computeScore: no visible global function definition for 'binomial'
computeScore: no visible global function definition for 'AIC'
convertToDr: no visible binding for global variable 'data'
myMean : medianM: no visible binding for global variable 'median'
Undefined global functions or variables:
  AIC binomial data glm median
Consider adding
  importFrom("stats", "AIC", "binomial", "glm", "median")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
computeDrStat 13.53   0.06   13.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
computeDrStat 14.41      0   14.41
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RTopper.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RTopper_1.28.0.tar.gz && rm -rf RTopper.buildbin-libdir && mkdir RTopper.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTopper.buildbin-libdir RTopper_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RTopper_1.28.0.zip && rm RTopper_1.28.0.tar.gz RTopper_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1094k  100 1094k    0     0  21.5M      0 --:--:-- --:--:-- --:--:-- 23.2M

install for i386

* installing *source* package 'RTopper' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTopper'
    finding HTML links ... done
    RTopper-package                         html  
    adjustPvalGSE                           html  
    finding level-2 HTML links ... done

    combineGSE                              html  
    computeDrStat                           html  
    convertToDr                             html  
    dat                                     html  
    fgsList                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6L6yAq/R.INSTALL15b8262d4594/RTopper/man/fgsList.Rd:37: file link 'org.Hs.eg' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6L6yAq/R.INSTALL15b8262d4594/RTopper/man/fgsList.Rd:41: file link 'GO' in package 'GO.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp6L6yAq/R.INSTALL15b8262d4594/RTopper/man/fgsList.Rd:42: file link 'KEGG' in package 'KEGG.db' does not exist and so has been treated as a topic
    gseResultsSep                           html  
    intScores                               html  
    pheno                                   html  
    runBatchGSE                             html  
    sepScores                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RTopper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTopper' as RTopper_1.28.0.zip
* DONE (RTopper)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RTopper' successfully unpacked and MD5 sums checked
In R CMD INSTALL